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As far back as I remember the turtles and their master's origins have differed; the four turtle brothers were turtles made humanoid, and splinter was master Yoshi made ratty....you know what I mean.

This was the case in all the TMNT related media I know of, except for in the 2003 cartoon. Doing some searching on the web, it seems that rat to humanoid is the 'original' origin story, and was changed for the 87 cartoon and Archie comic book series.

Why did this inconsistency come into the series? I was thinking the split in origins came from the 2003 cartoon, to accommodate the Utrom story line, and Yoshi being a guardian. But as Splinter's origins were originally from a rat this theory no longer makes hence.

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    Personally, I think the Mirage/Archie origin makes more sense: a human learning karate and teaching it to other humanoids instead of a rat learning it by mimicking it. But, in a story with mutants and alien brains, logic and plausibility aren't exactly the top priority.
    – phantom42
    Commented Nov 28, 2012 at 14:17
  • @phantom42 - Same. Which is why I was glad they went back to "Splinter was Yoshi" in the new Nick series.
    – System Down
    Commented Nov 28, 2012 at 18:05

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Disclaimer: These are personal musings and none of it is official.

As you said, there are two origin stories for Splinter:

  • Splinter was Hamato Yoshi's pet rat and learned Ninjutsu from him. He witnessed the death of his human master by the hands of Oroku Saki/Shredder in an incident that also sprung him free. This is the origin story used by the original Mirage comics, the new IDW relaunch comics, the live action movies, and the 2003 animated series.

  • Splinter was Hamato Yoshi himself, and was mutated into Splinter due to exposure to mutagenic ooze. This is the origin story for the 1987 animated series, the Archie comics, and the new 2012 animated series.

The first origin story is rather dark, as it involves the violent death of Hamato Yoshi. The series that followed that origin story tended to be dark in nature as well.

On the other hand, the second origin story is a lot lighter. Something that's reflected in the series that follow it.

So my guess would be that the origin story was first changed by the writers of the 1987 animated series to make the story lighter and more acceptable to the norms of the time. Remember that this was back in the 80's. It would be almost unthinkable to air a cartoon that featured such a dark back story. Other changes included making the Turtles into wise cracking, pizza munching, color coded, cute super heroes. The villains became buffoons. Less emphasis was placed on the ninja aspect of the TMNT. And even then it was deemed a bit too violent by some people (i.e. the UK censors).

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    +1 Exactly what I thought. The original work was so very dark. I am always amazed at their transformation into a televised kiddy cartoon. I am sure Eastman and Laird may have quietly questioned how far their creations had moved from their origins.
    – Thaddeus Howze
    Commented Nov 29, 2012 at 5:38
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    Teenage Mutant HERO Turtles!
    – Andres F.
    Commented Jul 7, 2013 at 15:03
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    Splinter being Yoshi's pet rat is NOT the origin in the current IDW relaunch comics. In the current comics, Hamato Yoshi and his four sons were killed at the hands of Oroku Saki(Shredder). They were then reincarnated as a rat and four turtles, which were mutated to become humanoid. Splinter retained most of his memories whereas the turtles mostly lost their memories of their previous lives.
    – numaroth
    Commented Aug 11, 2014 at 20:11

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